rs10489585

Variant names:

• chr1-184910171-A-T
• rs10489585
• NM_052966.4:c.56-10862T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_052966.4(NIBAN1):​c.56-10862T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0509 in 152,166 control chromosomes in the GnomAD database, including 369 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.051 (369 hom., cov: 32)
• Consequence: NIBAN1 NM_052966.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.325
• Publications: 1 publications found

Genes affected

NIBAN1 (HGNC:16784): (niban apoptosis regulator 1) This gene encodes a member of the family with sequence similarity 129 protein family. This gene is highly expressed in several cancer cells and may serve as a prognostic marker for certain cancers. The encoded protein may play a role in regulating p53-mediated apoptosis. [provided by RefSeq, Sep 2016]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NIBAN1	NM_052966.4	c.56-10862T>A		intron_variant	Intron 1 of 13	ENST00000367511.4	NP_443198.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NIBAN1	ENST00000367511.4	c.56-10862T>A		intron_variant	Intron 1 of 13	1	NM_052966.4	ENSP00000356481.3

Frequencies

GnomAD3 genomes AF: 0.0509 AC: 7738 AN: 152048 Hom.: 367 Cov.: 32

Gnomad AFR AF: 0.0115

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.0967

Gnomad EAS AF: 0.0645

Gnomad SAS AF: 0.0695

Gnomad FIN AF: 0.0413

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0477

Gnomad OTH AF: 0.0617

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0509 AC: 7743 AN: 152166 Hom.: 369 Cov.: 32 AF XY: 0.0524 AC XY: 3896 AN XY: 74380

African (AFR) AF: 0.0115 AC: 476 AN: 41542

American (AMR) AF: 0.157 AC: 2395 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0967 AC: 335 AN: 3466

East Asian (EAS) AF: 0.0637 AC: 328 AN: 5152

South Asian (SAS) AF: 0.0700 AC: 337 AN: 4816

European-Finnish (FIN) AF: 0.0413 AC: 438 AN: 10598

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0477 AC: 3243 AN: 68014

Other (OTH) AF: 0.0620 AC: 131 AN: 2112

Alfa AF: 0.0554 Hom.: 44

Bravo AF: 0.0603

Asia WGS AF: 0.0720 AC: 251 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.99
DANN	Benign	0.77
PhyloP100		-0.33
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10489585; hg19: chr1-184879304;